As an M.D./Ph.D. student, I have had the great opportunity to pursue my graduate studies in the laboratory of Dr. Jeremy Nathans. Our lab studies how blood vessels develop in the central nervous system. We have shown that two cell-surface proteins, Reck and Gpr124, are required for neurovascular development by activating signals associated with a protein called Wnt7a/7b (ligand) in endothelial cells. Furthermore, we demonstrate that Reck and Gpr124 operate by assembling into a multiprotein complex with Wnt7a/7b and another protein called Frizzled (receptor). In humans, there are 19 Wnts and 10 Frizzleds, but the extent of Wnt-Frizzled specificity and the biological roles that such specificity might play have largely remained open questions. Our work supports a novel paradigm for Wnt specificity and signifies the exciting possibility that receptor co-factors like Reck and Gpr124 exist for the other 17 Wnt ligands. Identifying these factors will be an important future direction for the field.

Cancer is fundamentally a disease of the genome. Numerous mutations accumulate in tumors, but only a few specific mutations actually “drive” the growth of cancer cells. We took a data science perspective to distinguish these key mutations by analyzing thousands of human cancer samples across 33 different types of cancer. Through developing novel statistical models that interpret the pattern of mutations observed in cancer, we found new genes and mutations associated with cancer. We found that although particular cancer-associated mutations may occur rarely in patients’ cancers, the overall prevalence of rare cancer-associated mutations suggest they have a critical, underappreciated role in cancer. This may have future implications for precision oncology, where interpretation of a cancer genome will need to be increasingly personalized, since key mutations in a patient’s cancer may have not been previously observed. This work was done in the Rachel Karchin lab (departments of Biomedical Engineering and Oncology and the Institute for Computational Medicine).

I completed my research in the laboratory of Dr. Doug Robinson in cell biology. My goal for my pulmonary fellowship training was to identify pathways that, for the first time, halt or reverse the damage seen in chronic obstructive lung disease (COPD) using basic science techniques and a model organism. As a lung disease, COPD is the third leading cause of death in the U.S., with cigarette smoking being a major risk factor. My work in the laboratory of Doug Robinson has led to the identification of new pathways in lung biology and laid the groundwork for my future early career investigations. Utilizing a discovery platform that extends from a model organism, Dictyostelium, which is a type of amoeba, to mouse and human models, we identified a protein called adenine nucleotide translocase (ANT) as protective against cigarette smoke. ANT transports a compound called adenosine triphosphate in mitochondria, the cell’s powerhouse. Surprisingly, we found it localizes to cilia, which are tiny, hairlike growths on cells, in the human airway, where it enhances airway hydration and protects ciliary function in the context of cigarette smoke. This provides a potential pathway for small molecule or gene therapies for COPD.

My goal is to understand how the neurons of the cerebellum, a region of the brain crucial for motor control and motor learning, contribute to the execution of voluntary eye movements. The cerebellum is a motor learning machine, correcting for movement errors, a process termed adaptation. In our work, we identified the neural substrates responsible for learning to correct eye movement errors. Understanding this adaptation process is critical for informing rehabilitation strategies for individuals with neurological damage or disease. This work was performed in the Laboratory for Computational Motor Control, under the direction of Dr. Reza Shadmehr, professor of biomedical engineering. In addition, much of the credit for this work goes to our close collaborators, Drs. Yoshiko Kojima and Robijanto Soetedjo from the University of Washington National Primate Center.

One research interest of the Semenza lab is to unravel how the HIF-1 gene plays an important role in critical aspects of cancer biology, including tumor angiogenesis, regulation of glucose and energy metabolism, invasion, metastasis and resistance to chemotherapy. Triple-negative breast cancers (TNBCs) are defined by the lack of expression in genes, including estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2. Chemotherapy is the primary established systemic treatment for TNBC, both in the early and advanced stages, with a durable response rate of less than 20 percent. Thus, it is critical to understand the properties of TNBC cells that survive chemotherapy in order to reduce patient mortality. Through my research, I identified how the hypoxia-inducible factors (HIFs) orchestrate both the intrinsic and acquired resistance in TNBC.

Stroke is one of the most common causes of physical disability worldwide, and the majority of people with stroke experience impairment of movement. Lesions to the motor areas in the brain following a stroke cause deficits in generating isolated finger movements, thus limiting basic daily functions. Unfortunately, conventional rehabilitation strategies fail to improve hand dexterity in the chronic stage of the stroke. In our study, we developed a novel motor skill training protocol and showed that individualized and intense motor skill training improves finger dexterity and basic hand functions, and reduces abnormal finger flexion synergy in people with chronic stroke. I am doing my research in the Human Brain Physiology and Stimulation Lab directed by Dr. Pablo Celnik at the Department of Physical Medicine and Rehabilitation.

Atopic dermatitis (AD), or eczema, is an inflammatory skin disease that affects 20 percent of children and about 5 percent of adults. Staphylococcus aureus colonization during AD contributes to skin inflammation, but the underlying mechanisms are unclear. We demonstrate that S. aureus-driven skin inflammation is mediated by bacterial toxin PMSα and the protein produced in our skin called IL-36. We found that normal mice develop scaly and inflamed skin after S. aureus colonization, but the genetically engineered mice lacking IL-36 activity had almost no skin inflammation. Therefore, IL-36 could be a potential biologic treatment target for AD. This research was done at Dr. Lloyd Miller’s lab in the Department of Dermatology.

Cells are the smallest unit of life that make up our body. However, a single cell is not just a single compartment; it is further divided into even smaller subcompartments, each of which is specialized in a certain biological function that enables the cell to maintain life. Among these various subcompartments, dropletlike organelles (also referred to as biomolecular condensates in recent reports) have been drawing more and more attention. They are rather newly discovered, the most dynamic class of subcellular compartments, whose behavior resembles that of liquid droplets or hydrogels. Without the surrounding lipid bilayer membrane, they can be assembled and disassembled within a relatively short period of time. These dynamic features are thought to be critical for the organelles for proper spatiotemporal regulation in a wide variety of biological contexts, including gene expression and stress response in many pathophysiologies. However, the mechanism of assembly and disassembly of the dropletlike organelles is unknown, in part due to the lack of techniques that can perturb the processes. Therefore, I developed a technique, iPOLYMER, that can manipulate the assembly of dropletlike organelles in living cells by chemicals or light irradiation. For this purpose, I used techniques in the synthetic biology field to induce sol-gel phase transition, one of the physicochemical mechanisms that have been related to the assembly of dropletlike organelles. Using iPOLYMER, I succeeded in synthetically mimicking stress granules, a well-known example of a dropletlike organelle, in living cells. These results suggested that sol-gel phase transition can be the underlying mechanism that regulates the assembly of the organelles. Furthermore, the results clearly demonstrated that iPOLYMER is a promising tool to elucidate the regulation of the dropletlike organelle assembly. Development of iPOLYMER can thus open up a new era in the research on dropletlike organelles, providing profound insights into both physiological and pathophysiological processes. The research was done in the Takanari Inoue lab (Department of Cell Biology, Center for Cell Dynamics).

Extant species have wildly different chromosome numbers, even among taxa with relatively similar genome size (e.g., insects). Humans have 23 pairs of chromosomes, while chimpanzee and other apes have 24. One human chromosome is a fusion product of the ancestral state. The jack jumper ant has the smallest chromosome number possible, with only one pair of chromosomes. This raises the interesting question: How well can a species tolerate a change in “n” without significant changes to genome content? Yeast is easy to engineer, and its 16 chromosomes have been fused before, but only up to 12. We have pushed the limits of chromosome fusion from 12 to two in Saccharomyces cerevisiae using CRISPR-Cas9. Surprisingly, the strain with only two chromosomes grows without major defects compared to wild type. In heterotypic crosses (n=8 X n=16), sporulation was arrested, with drastically reduced full tetrad formation detected and under 1% spore viability. These results indicate that as few as eight chromosome-chromosome fusion events suffice to isolate strains reproductively. The set of strains with varying chromosome number described here may be useful to tackle various and distinct biological questions; for example, aspects of recombination during meiosis, replication origin timing, or the role of yeast 3-D nuclear structure in transcriptional regulation or recombination donor preference, to name a few. I did the fusion chromosome project in the lab of Dr. Jef Boeke.

My work has been carried out in the Brem lab, also known as the Hunterian Neurosurgical Research Laboratory. Our work focuses on studying alternative and innovative therapeutics for adult and pediatric brain tumors. Specifically, our work has demonstrated that the antiviral drug ribavirin is effective as a potential therapeutic against the pediatric brain tumor atypical teratoid rhabdoid tumor (AT/RT). We have used preclinical in vitro and in vivo models to show that ribavirin has antitumoral efficacy as monotherapy and potential sensitizes AT/RT to currently used radiotherapy and chemotherapy. These are exciting findings, as children with AT/RTs are typically under the age of 3 years old, radiation therapy is not an option due to the developing nervous system and there is no standard chemotherapy regimen for these children.

The mammalian target of rapamycin complex 1 (mTORC1) is critical for both normal development and tumorigenesis, and is an attractive therapeutic target. In the Lotan lab we use biochemistry, imaging, microarrays and proteomics of the neonatal mouse skin to characterize the functions of mTORC1 in epithelial biology. In a recent study, we observed that mTORC1 loss was associated with a lethal skin barrier defect with blistering and impaired intercellular adhesion. These effects were due to upregulated Rho kinase (ROCK) signaling and a resulting failure to form desmosomes; structures that are critical to skin integrity. Our work provides a physiological basis for side effects such as delayed wound healing and skin eruptions that are frequently associated with mTORC1 inhibitors, and also highlights the TGFβ-ROCK pathway as a potentially druggable target, downstream of mTORC1 loss.

Understanding and manipulating bacterial growth is important for medical and pharmaceutical advances. How a bacterial cell divides is a complex biological process driven by the coordinated efforts of more than two dozen proteins. The most essential and conserved of these proteins is FtsZ, which forms a ringlike scaffold called a Z-ring. The Z-ring serves as a platform for the recruitment and organization of the division machinery. I discovered that the structure of the Z-ring and the assembly properties of FtsZ directly regulate cell division proteins. I also discovered and characterized a previously unknown link between FtsZ and the action of cell wall enzymes required for cell division—these enzymes are targets of penicillinlike antibiotics. In addition to providing mechanistic insights into the essential process of bacterial cell division, my project identifies molecular targets for manipulating bacterial cell growth. The cell-free reconstitution method that I developed to study FtsZ can be applied to study other multiprotein machineries that are essential for processes not just in bacteria but also more complex organisms, including humans. I did my research in Dr. Erin Goley’s lab, in the Department of Biological Chemistry. I also performed a significant portion of my experiments in Dr. Kiyoshi Mizuuchi’s lab at the National Institute of Diabetes and Digestive and Kidney Diseases.

Touch is an intrinsically active sense. As humans primarily use our hands to actively gather tactile information, mice use their whiskers to explore their environment. Leveraging the mouse whisker system as a model for active touch, we focused on understanding the mechanical sensitivity of a type of touch receptor called the Merkel cell-neurite complex. Employing optogenetics, electrophysiology and mechanical models, we found that these touch receptor neurons reliably encode features of both object touch and whisker position. This remarkable mechanical sensitivity supports the Merkel cell-neurite complex’s hypothesized role in perception of object shape. Furthermore, this work adds evidence that we should model touch and proprioception, the sense of body position, within a unified mechanical framework. These models could be particularly important for our basic understanding of touch perception, as well as engineering touch and proprioceptive feedback in prosthetics and robotics.

I did my research in the laboratory of Erika Matunis. This lab studies stem cell regulation using the fruit fly, Drosophila, testis stem cell niche as a model organism. I discovered that loss of the tumor suppressor gene retinoblastoma in niche cells, the cells that support and help maintain the stem cells, can cause niche cell proliferation, conversion of niche cells to stem cells and formation of ectopic niches. This finding is important because it shows that modulation of niche cells, not only the stem cells they support, can be important for tissue regeneration but can also lead to cancerous phenotypes when dysregulated.

Mitochondria are the cell’s powerhouses that provide the vast majority of all energy needed to run cellular activities. The energy comes in the form of a compound called adenosine triphosphate (ATP), which is made by a process referred to as oxidative phosphorylation. Oxidative phosphorylation is critical to tissues in the body that have a high energy demand and require the action of a transport protein, the adenosine diphosphate (ADP)/ATP carrier, which is what I study. This protein carries both ATP and ADP across the inner mitochondrial membrane in opposite directions to each other (ATP out of and ADP into the mitochondria), and the absence of this function is enough to stop ATP production by the mitochondrion. Proteins of the mitochondria and other cellular compartments are made either from cytoplasmic translation (majority of the proteins in the cell) or mitochondrial translation (few mitochondrial proteins). My research started with the aim of understanding how a mutation in the human ADP/ATP carrier caused a disease in a patient who presented with cardiomyopathy and myopathy (heart muscle and skeletal muscle dysfunction, respectively). Using a series of genetic and biochemical studies in yeast, we discovered that the activity of the ADP/ATP carrier is important for optimal mitochondrial translation. In the field of mitochondrial biology, this discovery is an important one. For more than two decades, the reason why mutations in the ADP/ATP carrier protein cause defective oxidative phosphorylation have been elusive. Our intriguing finding established a novel link between energy regulation and the synthesis of proteins in the mitochondrion. This research was done in the lab of Dr. Steven Claypool in the Department of Physiology.

As a postdoctoral fellow in the lab of Dr. Mingzhao Xing, I have been working on deciphering how genetic alterations contribute to thyroid tumorigenesis. We found that the genetic duet of BRAF and TERT promoter mutations identified the highest mortality risk in patients with papillary thyroid cancer and represented a robust molecular prognostic profile for this cancer. We explored the underlying molecular mechanism by focusing on the activation of mutant TERT by the BRAF V600E/MAP kinase pathway. We have demonstrated that in this process FOS, through acting as a novel transcriptional factor of GABPB promoter, increases the expression of GABPB, which in turn binds and activates the mutant TERT promoter. This functionally bridges the two oncogenes in cooperatively promoting oncogenesis, providing important cancer biological and clinical implications.

In Hal Dietz’s laboratory, I focused my doctoral research on pseudoxanthoma elasticum (PXE) — a rare genetic disorder of ectopic calcification, characterized by calcification in the skin, eyes and blood vessels. We discovered that defects in extracellular adenosine triphosphate metabolism drive ectopic calcification in PXE and identified a therapeutic intervention that successfully treated the disease both in vitro and in a PXE mouse model. We believe these findings will not only help patients with this rare disorder, but also inform our approaches to treating more common conditions, such as aortic valve calcification and chronic kidney disease-associated vascular calcification.

I work in the laboratory of Sinisa Urban, where we study the rhomboid family of enzymes. I determined how a malaria rhomboid enzyme recognizes its substrates and exploited that understanding to design a chemical inhibitor for this enzyme. This inhibitor, termed RiBn (for rhomboid-inhibiting boronate), blocked the invasion of parasites into red blood cells and cured cultures of malaria. This work demonstrated that the malaria rhomboid enzyme is both necessary for the pathogenesis of disease and therapeutically targetable.

Many secreted proteins circulating in the blood are responsible for the altered metabolic parameters in patients with obesity and diabetes. In Dr. Wong’s lab, we study a novel family of secreted proteins called CTRPs, many of which appear to be metabolically relevant. My project provided the first genetic and physiological evidence that one of these proteins, known as CTRP6, functions as a secreted metabolic/immune regulator linking obesity to adipose tissue inflammation and insulin resistance. The results are promising and can potentially guide researchers in the development of new therapeutic targets for the treatment of obesity and diabetes.

We study cell migration, a process that plays fundamental roles in normal physiology and disease conditions such as cancer metastasis. We are particularly interested in waves of cytoskeleton and signaling molecules observed near the surface of cells, and my project focused on how they are generated and what roles they play in cell migration. We developed tools to fine-tune wave propagation, and found that properties of these waves determine the types of protrusions that cells use to move around. With different types of protrusions, cells display distinct modes of motility. Our research provides causal evidence to support the idea that waves drive cell migration and shines light on why various cells move in different ways.

My work in Dr. Bert Vogelstein’s lab focused on the early detection of cancer, a leading cause of deaths worldwide with incidence projected to rise dramatically over the upcoming decades. Most cancer deaths result from tumors that have spread to distant sites. Thus, early detection would allow for the timely initiation of treatment while the tumor is still localized and offers tremendous potential for reducing mortality. We developed sensitive, sequencing-based assays to detect tumor-specific mutations as biomarkers for early disease. These assays have been successfully applied to diagnose various cancer types, such as ovarian and endometrial cancers, in easily collected bodily fluids, such as Pap smear fluid and plasma.